When simple sequence comparison fails: the cryptic case of the shared domains of the bacterial replication initiation proteins DnaB and DnaD
Author(s)Marston, Farhat Y.; Grainger, William H.; Smits, Wiep Klaas; Hopcroft, Nicholas H.; Green, Matthew; Hounslow, Andrea M.; Grossman, Alan D.; Craven, C. Jeremy; Soultanas, Panos; ... Show more Show less
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DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB Homology 1 and 2). Despite strong sequence divergence, many of the DNA-binding and oligomerization properties of these domains have been conserved. Although eluding simple sequence comparisons, the DDBH2 domains share the only strong sequence motif; an extremely highly conserved YxxxIxxxW sequence that contributes to DNA binding. Sequence alignments of DnaD alone fail to identify another key part of the DNA-binding module, since it includes a poorly conserved sequence, a solvent-exposed and somewhat unstable helix and a mobile segment. We show by NMR, in vitro mutagenesis and in vivo complementation experiments that the DNA-binding module of Bacillus subtilis DnaD comprises the YxxxIxxxW motif, the unstable helix and a portion of the mobile region, the latter two being essential for viability. These structural insights lead us to a re-evaluation of the oligomerization and DNA-binding properties of the DnaD and DnaB proteins.
DepartmentMassachusetts Institute of Technology. Department of Biology
Nucleic Acids Research
Oxford University Press
Marston, F. Y. et al. “When Simple Sequence Comparison Fails: The Cryptic Case of the Shared Domains of the Bacterial Replication Initiation Proteins DnaB and DnaD.” Nucleic Acids Research 38.20 (2010): 6930–6942. Web.
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